Starting phenix.real_space_refine on Mon Aug 25 08:08:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gnh_34164/08_2025/8gnh_34164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gnh_34164/08_2025/8gnh_34164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gnh_34164/08_2025/8gnh_34164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gnh_34164/08_2025/8gnh_34164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gnh_34164/08_2025/8gnh_34164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gnh_34164/08_2025/8gnh_34164.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16603 2.51 5 N 4333 2.21 5 O 5121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26171 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7816 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 55, 'TRANS': 976} Chain breaks: 7 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 12, 'ARG:plan': 7, 'TYR:plan': 6, 'TRP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 207 Chain: "B" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8083 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 56, 'TRANS': 1001} Chain breaks: 5 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 5, 'PHE:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 134 Chain: "C" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8096 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 56, 'TRANS': 991} Chain breaks: 7 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 903 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 769 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Restraints were copied for chains: N Time building chain proxies: 7.89, per 1000 atoms: 0.30 Number of scatterers: 26171 At special positions: 0 Unit cell: (138.205, 139.26, 229.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5121 8.00 N 4333 7.00 C 16603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.05 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.09 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM25735 O5 NAG A1301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1302 " - " ASN A1098 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A1074 " " NAG B1301 " - " ASN B1098 " " NAG B1303 " - " ASN B1134 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 165 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6298 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 45 sheets defined 22.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.926A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.538A pdb=" N ALA A 352 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.347A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.770A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 782 removed outlier: 4.705A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 898 through 910 removed outlier: 4.464A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.744A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 removed outlier: 3.717A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 985 through 1030 removed outlier: 4.796A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.620A pdb=" N THR A1120 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.534A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.115A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.881A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.951A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.903A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.565A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.927A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.517A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.632A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.530A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 941 removed outlier: 4.240A pdb=" N GLN B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.728A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.676A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.623A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.967A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 636 removed outlier: 4.082A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.645A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 removed outlier: 4.860A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 835 through 840 removed outlier: 3.945A pdb=" N ASP C 839 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.523A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 918 Processing helix chain 'C' and resid 919 through 938 removed outlier: 4.269A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.670A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1035 removed outlier: 4.105A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.603A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.796A pdb=" N PHE A 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.607A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.592A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.902A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.630A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.011A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.535A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.801A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.968A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.690A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.690A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 102 through 106 removed outlier: 4.822A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.478A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.689A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.877A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.877A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.427A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.596A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.878A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AC6, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC7, first strand: chain 'C' and resid 48 through 53 removed outlier: 7.344A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 63 through 65 removed outlier: 4.169A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 92 through 96 removed outlier: 4.231A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.948A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.938A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AD4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.528A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.206A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AD7, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AD8, first strand: chain 'C' and resid 576 through 578 Processing sheet with id=AD9, first strand: chain 'C' and resid 665 through 667 removed outlier: 7.050A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 713 through 719 removed outlier: 6.924A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 713 through 719 removed outlier: 6.924A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.161A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.620A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.620A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA L 84 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 20 through 24 732 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4325 1.30 - 1.44: 7525 1.44 - 1.59: 14744 1.59 - 1.73: 1 1.73 - 1.88: 138 Bond restraints: 26733 Sorted by residual: bond pdb=" CA PHE A 32 " pdb=" C PHE A 32 " ideal model delta sigma weight residual 1.522 1.431 0.091 1.08e-02 8.57e+03 7.14e+01 bond pdb=" C VAL B1104 " pdb=" O VAL B1104 " ideal model delta sigma weight residual 1.237 1.157 0.080 1.09e-02 8.42e+03 5.44e+01 bond pdb=" CA TYR C 707 " pdb=" C TYR C 707 " ideal model delta sigma weight residual 1.523 1.433 0.090 1.24e-02 6.50e+03 5.28e+01 bond pdb=" CA TYR B 279 " pdb=" C TYR B 279 " ideal model delta sigma weight residual 1.530 1.455 0.075 1.11e-02 8.12e+03 4.53e+01 bond pdb=" CA VAL B1104 " pdb=" C VAL B1104 " ideal model delta sigma weight residual 1.522 1.436 0.086 1.29e-02 6.01e+03 4.48e+01 ... (remaining 26728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 34710 3.28 - 6.56: 1425 6.56 - 9.84: 235 9.84 - 13.12: 59 13.12 - 16.40: 20 Bond angle restraints: 36449 Sorted by residual: angle pdb=" N ILE B 712 " pdb=" CA ILE B 712 " pdb=" C ILE B 712 " ideal model delta sigma weight residual 111.62 126.20 -14.58 7.90e-01 1.60e+00 3.40e+02 angle pdb=" N GLN C 580 " pdb=" CA GLN C 580 " pdb=" C GLN C 580 " ideal model delta sigma weight residual 111.03 96.07 14.96 1.11e+00 8.12e-01 1.82e+02 angle pdb=" N SER A 98 " pdb=" CA SER A 98 " pdb=" C SER A 98 " ideal model delta sigma weight residual 111.81 95.76 16.05 1.44e+00 4.82e-01 1.24e+02 angle pdb=" N SER C 31 " pdb=" CA SER C 31 " pdb=" C SER C 31 " ideal model delta sigma weight residual 113.15 124.84 -11.69 1.19e+00 7.06e-01 9.64e+01 angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 111.02 122.78 -11.76 1.22e+00 6.72e-01 9.29e+01 ... (remaining 36444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.44: 15398 28.44 - 56.87: 903 56.87 - 85.31: 99 85.31 - 113.75: 46 113.75 - 142.18: 1 Dihedral angle restraints: 16447 sinusoidal: 6672 harmonic: 9775 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 15.45 77.55 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -8.81 -77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -159.78 73.78 1 1.00e+01 1.00e-02 6.92e+01 ... (remaining 16444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.181: 4301 1.181 - 2.362: 3 2.362 - 3.542: 3 3.542 - 4.723: 0 4.723 - 5.904: 1 Chirality restraints: 4308 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 3.50 -5.90 2.00e-01 2.50e+01 8.71e+02 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 0.58 -2.98 2.00e-01 2.50e+01 2.22e+02 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 0.57 -2.97 2.00e-01 2.50e+01 2.20e+02 ... (remaining 4305 not shown) Planarity restraints: 4714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.311 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG A1301 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.480 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.308 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG B1304 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.452 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.086 2.00e-02 2.50e+03 7.99e-02 7.98e+01 pdb=" CG ASN B 603 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.099 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.097 2.00e-02 2.50e+03 ... (remaining 4711 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 12 2.15 - 2.84: 10832 2.84 - 3.52: 38566 3.52 - 4.21: 61420 4.21 - 4.90: 101597 Nonbonded interactions: 212427 Sorted by model distance: nonbonded pdb=" ND2 ASN A 801 " pdb=" O5 NAG A1301 " model vdw 1.460 3.120 nonbonded pdb=" OD1 ASN B 282 " pdb=" C1 NAG B1306 " model vdw 1.755 2.776 nonbonded pdb=" OD1 ASN C1134 " pdb=" C1 NAG C1302 " model vdw 1.809 3.470 nonbonded pdb=" OD1 ASN B 282 " pdb=" O5 NAG B1306 " model vdw 1.893 3.040 nonbonded pdb=" OD1 ASN A 801 " pdb=" C1 NAG A1301 " model vdw 2.031 3.470 ... (remaining 212422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 131 or (resid 132 through 133 and (name N or na \ me CA or name C or name O or name CB )) or resid 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 159 or (resid 1 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 172 or resid 186 through 212 or (resid 213 through 214 and (name N or name CA o \ r name C or name O or name CB )) or resid 215 through 217 or (resid 218 and (nam \ e N or name CA or name C or name O or name CB )) or resid 219 through 250 or res \ id 265 through 275 or (resid 276 through 281 and (name N or name CA or name C or \ name O or name CB )) or resid 282 through 318 or (resid 319 and (name N or name \ CA or name C or name O or name CB )) or resid 320 through 326 or (resid 327 thr \ ough 329 and (name N or name CA or name C or name O or name CB )) or resid 330 t \ hrough 334 or (resid 335 and (name N or name CA or name C or name O or name CB ) \ ) or resid 336 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O or name CB )) or resid 339 or (resid 340 and (name N or name CA or name C or \ name O or name CB )) or resid 341 or (resid 342 and (name N or name CA or name \ C or name O or name CB )) or resid 343 through 345 or (resid 346 and (name N or \ name CA or name C or name O or name CB )) or resid 347 through 363 or (resid 364 \ through 365 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 66 through 367 or (resid 368 and (name N or name CA or name C or name O or name \ CB )) or resid 369 through 387 or (resid 388 and (name N or name CA or name C or \ name O or name CB )) or resid 389 through 428 or (resid 429 and (name N or name \ CA or name C or name O or name CB )) or resid 430 through 452 or (resid 453 and \ (name N or name CA or name C or name O or name CB )) or resid 454 through 460 o \ r (resid 461 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 62 through 516 or (resid 517 and (name N or name CA or name C or name O or name \ CB )) or resid 518 through 527 or (resid 528 and (name N or name CA or name C or \ name O or name CB )) or resid 529 through 828 or resid 850 through 981 or (resi \ d 982 and (name N or name CA or name C or name O or name CB )) or resid 983 thro \ ugh 1080 or (resid 1081 and (name N or name CA or name C or name O or name CB )) \ or resid 1082 through 1096 or (resid 1097 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1098 through 1099 or (resid 1100 through 1107 and ( \ name N or name CA or name C or name O or name CB )) or resid 1108 or (resid 1109 \ and (name N or name CA or name C or name O or name CB )) or resid 1110 through \ 1134 or (resid 1135 and (name N or name CA or name C or name O or name CB )) or \ resid 1136 through 1309)) selection = (chain 'B' and (resid 27 through 30 or (resid 31 through 32 and (name N or name \ CA or name C or name O or name CB )) or resid 33 or (resid 34 and (name N or nam \ e CA or name C or name O or name CB )) or resid 35 or (resid 36 through 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 54 or (r \ esid 55 and (name N or name CA or name C or name O or name CB )) or resid 56 thr \ ough 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or \ resid 59 through 63 or (resid 64 through 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 through 95 or (resid 96 and (name N or name CA \ or name C or name O or name CB )) or resid 97 through 100 or (resid 101 through \ 102 and (name N or name CA or name C or name O or name CB )) or resid 103 throu \ gh 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or \ resid 115 through 117 or (resid 118 and (name N or name CA or name C or name O \ or name CB )) or resid 119 through 191 or (resid 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 194 or (resid 195 and (name N \ or name CA or name C or name O or name CB )) or resid 196 through 200 or (resid \ 201 and (name N or name CA or name C or name O or name CB )) or resid 202 throu \ gh 212 or (resid 213 through 214 and (name N or name CA or name C or name O or n \ ame CB )) or resid 215 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 222 or (resid 223 and (name N or \ name CA or name C or name O or name CB )) or resid 224 through 236 or (resid 237 \ and (name N or name CA or name C or name O or name CB )) or resid 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throu \ gh 250 or resid 265 through 326 or (resid 327 through 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330 through 334 or (resid 335 and (n \ ame N or name CA or name C or name O or name CB )) or resid 336 through 337 or ( \ resid 338 and (name N or name CA or name C or name O or name CB )) or resid 339 \ through 341 or (resid 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 345 or (resid 346 and (name N or name CA or name C or na \ me O or name CB )) or resid 347 through 348 or (resid 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 or (resid 351 through 352 and (n \ ame N or name CA or name C or name O or name CB )) or resid 353 through 391 or ( \ resid 392 and (name N or name CA or name C or name O or name CB )) or resid 393 \ through 399 or (resid 400 and (name N or name CA or name C or name O or name CB \ )) or resid 401 through 408 or (resid 409 and (name N or name CA or name C or na \ me O or name CB )) or resid 410 through 438 or (resid 439 and (name N or name CA \ or name C or name O or name CB )) or resid 440 through 441 or (resid 442 and (n \ ame N or name CA or name C or name O or name CB )) or resid 450 through 496 or ( \ resid 497 through 498 and (name N or name CA or name C or name O or name CB )) o \ r resid 499 through 504 or (resid 505 and (name N or name CA or name C or name O \ or name CB )) or resid 506 through 507 or (resid 508 through 509 and (name N or \ name CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name \ N or name CA or name C or name O or name CB )) or resid 512 through 540 or (resi \ d 541 and (name N or name CA or name C or name O or name CB )) or resid 542 thro \ ugh 550 or (resid 551 and (name N or name CA or name C or name O or name CB )) o \ r resid 552 or (resid 553 through 555 and (name N or name CA or name C or name O \ or name CB )) or resid 556 through 582 or (resid 583 and (name N or name CA or \ name C or name O or name CB )) or resid 584 or (resid 585 through 586 and (name \ N or name CA or name C or name O or name CB )) or resid 587 through 736 or (resi \ d 737 and (name N or name CA or name C or name O or name CB )) or resid 738 thro \ ugh 815 or (resid 816 and (name N or name CA or name C or name O or name CB )) o \ r resid 817 through 828 or resid 850 through 857 or (resid 858 and (name N or na \ me CA or name C or name O or name CB )) or resid 859 through 1096 or (resid 1097 \ and (name N or name CA or name C or name O or name CB )) or resid 1098 through \ 1099 or (resid 1100 through 1107 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1108 or (resid 1109 and (name N or name CA or name C or name \ O or name CB )) or resid 1110 through 1309)) selection = (chain 'C' and (resid 27 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 35 or (resid 36 through 37 and (na \ me N or name CA or name C or name O or name CB )) or resid 38 through 54 or (res \ id 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throu \ gh 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or r \ esid 59 through 63 or (resid 64 through 65 and (name N or name CA or name C or n \ ame O or name CB )) or resid 66 through 95 or (resid 96 and (name N or name CA o \ r name C or name O or name CB )) or resid 97 through 100 or (resid 101 through 1 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 103 through \ 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or r \ esid 115 through 117 or (resid 118 and (name N or name CA or name C or name O or \ name CB )) or resid 119 through 131 or (resid 132 through 133 and (name N or na \ me CA or name C or name O or name CB )) or resid 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 159 or (resid 1 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 161 through \ 190 or (resid 191 through 192 and (name N or name CA or name C or name O or nam \ e CB )) or resid 193 or (resid 194 through 195 and (name N or name CA or name C \ or name O or name CB )) or resid 196 through 199 or (resid 200 through 201 and ( \ name N or name CA or name C or name O or name CB )) or resid 202 through 213 or \ (resid 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 222 or (resid 223 and (name N or name CA or name C or name O or name CB \ )) or resid 224 through 236 or (resid 237 and (name N or name CA or name C or n \ ame O or name CB )) or resid 238 or (resid 239 and (name N or name CA or name C \ or name O or name CB )) or resid 240 or (resid 241 and (name N or name CA or nam \ e C or name O or name CB )) or resid 242 through 250 or resid 265 through 275 or \ (resid 276 through 281 and (name N or name CA or name C or name O or name CB )) \ or resid 282 through 318 or (resid 319 and (name N or name CA or name C or name \ O or name CB )) or resid 320 through 339 or (resid 340 and (name N or name CA o \ r name C or name O or name CB )) or resid 341 through 348 or (resid 349 and (nam \ e N or name CA or name C or name O or name CB )) or resid 350 or (resid 351 thro \ ugh 352 and (name N or name CA or name C or name O or name CB )) or resid 353 th \ rough 363 or (resid 364 through 365 and (name N or name CA or name C or name O o \ r name CB )) or resid 366 through 367 or (resid 368 and (name N or name CA or na \ me C or name O or name CB )) or resid 369 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 391 or (resid \ 392 and (name N or name CA or name C or name O or name CB )) or resid 393 throug \ h 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) or \ resid 401 through 402 or (resid 403 and (name N or name CA or name C or name O o \ r name CB )) or resid 404 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 428 or (resid 429 and (name N \ or name CA or name C or name O or name CB )) or resid 430 through 438 or (resid \ 439 and (name N or name CA or name C or name O or name CB )) or resid 440 throug \ h 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 452 or (resid 453 and (name N or name CA or name C or name O o \ r name CB )) or resid 454 through 460 or (resid 461 and (name N or name CA or na \ me C or name O or name CB )) or resid 462 through 494 or (resid 495 and (name N \ or name CA or name C or name O or name CB )) or resid 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 throug \ h 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 507 or (resid 508 through 509 and (name N or name CA or name C \ or name O or name CB )) or resid 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 514 or (resid 515 through 517 \ and (name N or name CA or name C or name O or name CB )) or resid 518 through 52 \ 7 or (resid 528 and (name N or name CA or name C or name O or name CB )) or resi \ d 529 through 540 or (resid 541 and (name N or name CA or name C or name O or na \ me CB )) or resid 542 through 550 or (resid 551 and (name N or name CA or name C \ or name O or name CB )) or resid 552 or (resid 553 through 555 and (name N or n \ ame CA or name C or name O or name CB )) or resid 556 through 582 or (resid 583 \ and (name N or name CA or name C or name O or name CB )) or resid 584 or (resid \ 585 through 586 and (name N or name CA or name C or name O or name CB )) or resi \ d 587 through 815 or (resid 816 and (name N or name CA or name C or name O or na \ me CB )) or resid 817 through 828 or resid 834 or resid 851 through 857 or (resi \ d 858 and (name N or name CA or name C or name O or name CB )) or resid 859 thro \ ugh 981 or (resid 982 and (name N or name CA or name C or name O or name CB )) o \ r resid 983 through 1080 or (resid 1081 and (name N or name CA or name C or name \ O or name CB )) or resid 1082 through 1106 or (resid 1107 and (name N or name C \ A or name C or name O or name CB )) or resid 1108 through 1134 or (resid 1135 an \ d (name N or name CA or name C or name O or name CB )) or resid 1136 through 130 \ 9)) } ncs_group { reference = chain 'D' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.160 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.869 26802 Z= 0.769 Angle : 1.719 48.017 36614 Z= 0.948 Chirality : 0.166 5.904 4308 Planarity : 0.011 0.272 4689 Dihedral : 17.786 142.184 10023 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 49.62 Ramachandran Plot: Outliers : 4.01 % Allowed : 20.32 % Favored : 75.67 % Rotamer: Outliers : 8.96 % Allowed : 3.41 % Favored : 87.62 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.10 (0.12), residues: 3317 helix: -2.06 (0.17), residues: 675 sheet: -2.98 (0.23), residues: 457 loop : -4.22 (0.11), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 44 TYR 0.082 0.003 TYR A 91 PHE 0.072 0.004 PHE B 643 TRP 0.044 0.004 TRP B 436 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01221 (26733) covalent geometry : angle 1.56439 (36449) SS BOND : bond 0.01206 ( 42) SS BOND : angle 2.51540 ( 84) hydrogen bonds : bond 0.19708 ( 707) hydrogen bonds : angle 9.41120 ( 1977) link_BETA1-4 : bond 0.06591 ( 2) link_BETA1-4 : angle 9.21541 ( 6) link_NAG-ASN : bond 0.20326 ( 25) link_NAG-ASN : angle 15.45600 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 123 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.5897 (m110) REVERT: A 91 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6278 (p90) REVERT: A 97 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7285 (mtmt) REVERT: A 229 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 325 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7980 (p) REVERT: A 326 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6419 (mt) REVERT: A 429 PHE cc_start: 0.7949 (t80) cc_final: 0.7523 (t80) REVERT: A 453 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7766 (p90) REVERT: A 859 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 901 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8906 (tm-30) REVERT: B 215 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.4898 (m-30) REVERT: B 304 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8749 (mmtt) REVERT: B 740 MET cc_start: 0.9102 (tpt) cc_final: 0.8675 (tpp) REVERT: B 954 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: B 960 ASN cc_start: 0.8695 (m-40) cc_final: 0.8411 (t0) REVERT: C 86 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7736 (t80) REVERT: C 242 LEU cc_start: 0.8606 (mp) cc_final: 0.8010 (mp) REVERT: C 365 TYR cc_start: 0.9417 (m-80) cc_final: 0.9191 (m-80) REVERT: C 582 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9283 (mm) REVERT: C 1031 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: C 1033 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9162 (p) REVERT: L 78 LEU cc_start: -0.1293 (tp) cc_final: -0.1516 (mt) outliers start: 252 outliers final: 132 residues processed: 365 average time/residue: 0.1646 time to fit residues: 97.4862 Evaluate side-chains 225 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 77 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain L residue 46 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 125 ASN B 134 GLN B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 919 ASN B 920 GLN B 954 GLN B1071 GLN B1074 ASN B1106 GLN C 87 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN H 39 GLN H 52 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.084130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.057358 restraints weight = 119529.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059261 restraints weight = 55851.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.060457 restraints weight = 35257.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061171 restraints weight = 26635.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.061600 restraints weight = 22484.256| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26802 Z= 0.191 Angle : 0.977 22.073 36614 Z= 0.472 Chirality : 0.055 0.472 4308 Planarity : 0.006 0.072 4689 Dihedral : 13.558 101.178 4620 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.65 % Favored : 84.93 % Rotamer: Outliers : 5.05 % Allowed : 10.03 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.01 (0.13), residues: 3317 helix: -0.27 (0.20), residues: 700 sheet: -2.89 (0.21), residues: 523 loop : -3.71 (0.11), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.033 0.002 TYR A 707 PHE 0.030 0.002 PHE A 59 TRP 0.031 0.002 TRP A 353 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00415 (26733) covalent geometry : angle 0.93814 (36449) SS BOND : bond 0.00416 ( 42) SS BOND : angle 1.83615 ( 84) hydrogen bonds : bond 0.05263 ( 707) hydrogen bonds : angle 6.51746 ( 1977) link_BETA1-4 : bond 0.02617 ( 2) link_BETA1-4 : angle 3.01806 ( 6) link_NAG-ASN : bond 0.00911 ( 25) link_NAG-ASN : angle 5.77351 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 124 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.6792 (m110) REVERT: A 206 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8451 (tptp) REVERT: A 229 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 326 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7416 (tt) REVERT: A 429 PHE cc_start: 0.8214 (t80) cc_final: 0.7422 (t80) REVERT: A 580 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: A 587 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6953 (tp) REVERT: A 740 MET cc_start: 0.8309 (tmm) cc_final: 0.7775 (tmm) REVERT: A 802 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8360 (p90) REVERT: B 215 ASP cc_start: 0.5120 (OUTLIER) cc_final: 0.4749 (m-30) REVERT: B 235 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7366 (mp) REVERT: B 304 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8670 (mmmt) REVERT: B 380 TYR cc_start: 0.8073 (m-80) cc_final: 0.7784 (m-80) REVERT: B 468 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7600 (mp) REVERT: B 740 MET cc_start: 0.9143 (tpt) cc_final: 0.8701 (tpp) REVERT: B 776 LYS cc_start: 0.9323 (tppp) cc_final: 0.9090 (tppt) REVERT: B 960 ASN cc_start: 0.8674 (m-40) cc_final: 0.8418 (t0) REVERT: B 1071 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8047 (tp40) REVERT: C 238 PHE cc_start: 0.8478 (p90) cc_final: 0.8086 (p90) REVERT: C 269 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: C 365 TYR cc_start: 0.9406 (m-80) cc_final: 0.9159 (m-80) REVERT: C 718 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8274 (p90) REVERT: C 1107 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7482 (tpm170) REVERT: L 53 ASN cc_start: 0.6088 (OUTLIER) cc_final: 0.5626 (p0) REVERT: L 97 PHE cc_start: 0.8078 (t80) cc_final: 0.7785 (t80) outliers start: 142 outliers final: 75 residues processed: 257 average time/residue: 0.1666 time to fit residues: 70.0884 Evaluate side-chains 176 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 85 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 266 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 312 optimal weight: 30.0000 chunk 146 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 248 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 184 optimal weight: 0.0030 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 122 ASN B 331 ASN C 99 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 53 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.082155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055029 restraints weight = 120570.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.056801 restraints weight = 57078.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.057959 restraints weight = 36693.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.058659 restraints weight = 27891.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059080 restraints weight = 23670.914| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26802 Z= 0.184 Angle : 0.870 28.367 36614 Z= 0.414 Chirality : 0.053 1.061 4308 Planarity : 0.006 0.075 4689 Dihedral : 11.251 85.031 4478 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.86 % Favored : 84.87 % Rotamer: Outliers : 4.45 % Allowed : 13.37 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.38 (0.14), residues: 3317 helix: 0.71 (0.20), residues: 691 sheet: -2.71 (0.20), residues: 601 loop : -3.38 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.028 0.002 TYR A 707 PHE 0.022 0.002 PHE B 490 TRP 0.021 0.002 TRP A 353 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00408 (26733) covalent geometry : angle 0.81660 (36449) SS BOND : bond 0.00513 ( 42) SS BOND : angle 1.26379 ( 84) hydrogen bonds : bond 0.04529 ( 707) hydrogen bonds : angle 5.99272 ( 1977) link_BETA1-4 : bond 0.01769 ( 2) link_BETA1-4 : angle 2.82451 ( 6) link_NAG-ASN : bond 0.01185 ( 25) link_NAG-ASN : angle 6.54789 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 96 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.6866 (m110) REVERT: A 206 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8403 (tptp) REVERT: A 229 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8556 (pp) REVERT: A 326 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7201 (mt) REVERT: A 336 CYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6538 (t) REVERT: A 378 LYS cc_start: 0.7996 (tptp) cc_final: 0.7752 (tptp) REVERT: A 421 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: A 429 PHE cc_start: 0.8260 (t80) cc_final: 0.7625 (t80) REVERT: A 433 VAL cc_start: 0.8667 (m) cc_final: 0.8452 (m) REVERT: A 460 ASN cc_start: 0.8904 (p0) cc_final: 0.8462 (m-40) REVERT: A 580 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: A 587 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7301 (tp) REVERT: A 740 MET cc_start: 0.8334 (tmm) cc_final: 0.7686 (tmm) REVERT: A 802 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.7952 (p90) REVERT: B 69 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6197 (m-70) REVERT: B 215 ASP cc_start: 0.5253 (OUTLIER) cc_final: 0.4794 (m-30) REVERT: B 304 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8913 (mmmt) REVERT: B 380 TYR cc_start: 0.8134 (m-80) cc_final: 0.7797 (m-80) REVERT: B 468 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7683 (mp) REVERT: B 740 MET cc_start: 0.9165 (tpt) cc_final: 0.8755 (tpp) REVERT: B 960 ASN cc_start: 0.8810 (m-40) cc_final: 0.8582 (t0) REVERT: B 1071 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7994 (tp40) REVERT: C 238 PHE cc_start: 0.8624 (p90) cc_final: 0.8113 (p90) REVERT: C 269 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: C 365 TYR cc_start: 0.9440 (m-80) cc_final: 0.9155 (m-10) REVERT: C 387 LEU cc_start: 0.8912 (mt) cc_final: 0.8694 (mm) REVERT: C 697 MET cc_start: 0.8689 (ttp) cc_final: 0.8440 (ttm) REVERT: C 718 PHE cc_start: 0.9481 (OUTLIER) cc_final: 0.8304 (p90) REVERT: C 921 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8194 (tptt) REVERT: L 97 PHE cc_start: 0.8346 (t80) cc_final: 0.8004 (t80) outliers start: 125 outliers final: 63 residues processed: 214 average time/residue: 0.1714 time to fit residues: 60.4428 Evaluate side-chains 153 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 73 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 125 optimal weight: 4.9990 chunk 227 optimal weight: 0.7980 chunk 214 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 154 optimal weight: 0.0370 chunk 249 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 276 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 315 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 125 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.082420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.056068 restraints weight = 119386.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.058616 restraints weight = 61704.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.058732 restraints weight = 32948.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059017 restraints weight = 27054.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.059052 restraints weight = 26565.500| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26802 Z= 0.144 Angle : 0.804 25.219 36614 Z= 0.381 Chirality : 0.050 0.784 4308 Planarity : 0.005 0.078 4689 Dihedral : 10.126 75.286 4448 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.57 % Favored : 87.16 % Rotamer: Outliers : 3.59 % Allowed : 15.01 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.99 (0.14), residues: 3317 helix: 1.23 (0.21), residues: 675 sheet: -2.38 (0.21), residues: 572 loop : -3.20 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.025 0.001 TYR A 707 PHE 0.037 0.001 PHE C 855 TRP 0.015 0.001 TRP B 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00321 (26733) covalent geometry : angle 0.75157 (36449) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.18995 ( 84) hydrogen bonds : bond 0.04088 ( 707) hydrogen bonds : angle 5.67787 ( 1977) link_BETA1-4 : bond 0.01284 ( 2) link_BETA1-4 : angle 1.99601 ( 6) link_NAG-ASN : bond 0.00919 ( 25) link_NAG-ASN : angle 6.23066 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 82 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.6859 (m110) REVERT: A 229 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8711 (pt) REVERT: A 378 LYS cc_start: 0.7661 (tptp) cc_final: 0.7429 (tptp) REVERT: A 421 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: A 429 PHE cc_start: 0.8234 (t80) cc_final: 0.7561 (t80) REVERT: A 433 VAL cc_start: 0.8552 (m) cc_final: 0.8327 (m) REVERT: A 460 ASN cc_start: 0.8931 (p0) cc_final: 0.8465 (m-40) REVERT: A 562 PHE cc_start: 0.6695 (p90) cc_final: 0.6372 (p90) REVERT: A 587 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7402 (tp) REVERT: A 740 MET cc_start: 0.8386 (tmm) cc_final: 0.7685 (tmm) REVERT: A 802 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.7766 (p90) REVERT: B 69 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6291 (m-70) REVERT: B 104 TRP cc_start: 0.7127 (OUTLIER) cc_final: 0.5963 (p-90) REVERT: B 215 ASP cc_start: 0.5295 (OUTLIER) cc_final: 0.4882 (m-30) REVERT: B 468 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 740 MET cc_start: 0.9199 (tpt) cc_final: 0.8807 (tpp) REVERT: B 776 LYS cc_start: 0.9430 (tppp) cc_final: 0.9170 (tppt) REVERT: B 1071 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8053 (tp40) REVERT: C 238 PHE cc_start: 0.8543 (p90) cc_final: 0.8233 (p90) REVERT: C 365 TYR cc_start: 0.9466 (m-80) cc_final: 0.9145 (m-10) REVERT: C 387 LEU cc_start: 0.8882 (mt) cc_final: 0.8675 (mm) REVERT: C 697 MET cc_start: 0.8642 (ttp) cc_final: 0.8205 (ttp) REVERT: C 921 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8181 (tptt) REVERT: L 97 PHE cc_start: 0.8249 (t80) cc_final: 0.7746 (t80) outliers start: 101 outliers final: 52 residues processed: 175 average time/residue: 0.1545 time to fit residues: 44.6062 Evaluate side-chains 133 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 70 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 88 optimal weight: 4.9990 chunk 305 optimal weight: 0.7980 chunk 333 optimal weight: 40.0000 chunk 230 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 125 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 325 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.081846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.054492 restraints weight = 120443.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.056335 restraints weight = 57445.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.057466 restraints weight = 37020.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058143 restraints weight = 28241.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058563 restraints weight = 23984.703| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26802 Z= 0.155 Angle : 0.778 22.325 36614 Z= 0.370 Chirality : 0.049 0.664 4308 Planarity : 0.005 0.072 4689 Dihedral : 9.195 71.078 4414 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.93 % Favored : 86.89 % Rotamer: Outliers : 3.09 % Allowed : 16.15 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.14), residues: 3317 helix: 1.40 (0.21), residues: 674 sheet: -2.32 (0.21), residues: 571 loop : -3.03 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.025 0.001 TYR A 707 PHE 0.036 0.001 PHE C 855 TRP 0.015 0.001 TRP B 104 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00346 (26733) covalent geometry : angle 0.72800 (36449) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.64475 ( 84) hydrogen bonds : bond 0.03946 ( 707) hydrogen bonds : angle 5.54222 ( 1977) link_BETA1-4 : bond 0.01029 ( 2) link_BETA1-4 : angle 2.23719 ( 6) link_NAG-ASN : bond 0.00820 ( 25) link_NAG-ASN : angle 5.85067 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 80 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.6830 (m110) REVERT: A 421 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: A 429 PHE cc_start: 0.8311 (t80) cc_final: 0.7891 (t80) REVERT: A 460 ASN cc_start: 0.8924 (p0) cc_final: 0.8565 (m-40) REVERT: A 562 PHE cc_start: 0.6729 (p90) cc_final: 0.6426 (p90) REVERT: A 587 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7542 (tp) REVERT: A 740 MET cc_start: 0.8466 (tmm) cc_final: 0.7730 (tmm) REVERT: A 802 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.7721 (p90) REVERT: A 851 CYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8255 (t) REVERT: B 69 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6210 (m-70) REVERT: B 104 TRP cc_start: 0.7105 (OUTLIER) cc_final: 0.5924 (p-90) REVERT: B 215 ASP cc_start: 0.5407 (OUTLIER) cc_final: 0.4949 (m-30) REVERT: B 740 MET cc_start: 0.9171 (tpt) cc_final: 0.8845 (tpp) REVERT: B 776 LYS cc_start: 0.9454 (tppp) cc_final: 0.9250 (tppt) REVERT: C 201 PHE cc_start: 0.8040 (t80) cc_final: 0.7621 (t80) REVERT: C 697 MET cc_start: 0.8701 (ttp) cc_final: 0.8370 (ttm) REVERT: C 921 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8251 (tptt) REVERT: L 78 LEU cc_start: -0.0310 (tp) cc_final: -0.0883 (mt) REVERT: L 97 PHE cc_start: 0.8287 (t80) cc_final: 0.7845 (t80) outliers start: 87 outliers final: 53 residues processed: 164 average time/residue: 0.1551 time to fit residues: 42.7374 Evaluate side-chains 132 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 70 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 99 optimal weight: 0.0670 chunk 157 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 chunk 234 optimal weight: 0.0970 chunk 214 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 270 optimal weight: 0.7980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN B 125 ASN B 920 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1036 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.082585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055755 restraints weight = 119248.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.057557 restraints weight = 56633.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.058724 restraints weight = 36130.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.059409 restraints weight = 27380.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.059850 restraints weight = 23250.640| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26802 Z= 0.121 Angle : 0.745 20.121 36614 Z= 0.350 Chirality : 0.048 0.618 4308 Planarity : 0.005 0.065 4689 Dihedral : 8.480 66.940 4396 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.55 % Favored : 88.27 % Rotamer: Outliers : 2.77 % Allowed : 16.86 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.14), residues: 3317 helix: 1.51 (0.21), residues: 685 sheet: -1.98 (0.21), residues: 584 loop : -2.90 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1091 TYR 0.023 0.001 TYR A 707 PHE 0.030 0.001 PHE C 855 TRP 0.013 0.001 TRP B 104 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00265 (26733) covalent geometry : angle 0.69520 (36449) SS BOND : bond 0.00521 ( 42) SS BOND : angle 1.51301 ( 84) hydrogen bonds : bond 0.03622 ( 707) hydrogen bonds : angle 5.27872 ( 1977) link_BETA1-4 : bond 0.01092 ( 2) link_BETA1-4 : angle 3.15523 ( 6) link_NAG-ASN : bond 0.00890 ( 25) link_NAG-ASN : angle 5.68994 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 90 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.6840 (m110) REVERT: A 231 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 378 LYS cc_start: 0.8118 (tptp) cc_final: 0.7842 (tptp) REVERT: A 402 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7777 (pt) REVERT: A 421 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7852 (m-10) REVERT: A 429 PHE cc_start: 0.8565 (t80) cc_final: 0.7838 (t80) REVERT: A 461 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5916 (pt) REVERT: A 740 MET cc_start: 0.8419 (tmm) cc_final: 0.7821 (tmm) REVERT: A 802 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7766 (p90) REVERT: A 851 CYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8475 (t) REVERT: A 1002 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8619 (tm-30) REVERT: B 69 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6199 (m-70) REVERT: B 104 TRP cc_start: 0.6933 (OUTLIER) cc_final: 0.5812 (p-90) REVERT: B 115 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7201 (mm110) REVERT: B 215 ASP cc_start: 0.5239 (OUTLIER) cc_final: 0.4769 (m-30) REVERT: B 380 TYR cc_start: 0.8157 (m-80) cc_final: 0.7827 (m-80) REVERT: B 574 ASP cc_start: 0.8460 (m-30) cc_final: 0.8149 (m-30) REVERT: B 740 MET cc_start: 0.9180 (tpt) cc_final: 0.8863 (tpp) REVERT: B 776 LYS cc_start: 0.9491 (tppp) cc_final: 0.9260 (tppt) REVERT: C 201 PHE cc_start: 0.7935 (t80) cc_final: 0.7482 (t80) REVERT: C 488 CYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5618 (t) REVERT: C 697 MET cc_start: 0.8720 (ttp) cc_final: 0.8346 (ttm) REVERT: C 921 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8265 (tptt) REVERT: H 110 GLU cc_start: 0.7639 (pm20) cc_final: 0.7268 (pm20) REVERT: L 63 SER cc_start: 0.3321 (OUTLIER) cc_final: 0.3051 (m) REVERT: L 78 LEU cc_start: -0.0358 (tp) cc_final: -0.0968 (mt) REVERT: L 79 GLU cc_start: 0.5532 (mt-10) cc_final: 0.5235 (mp0) outliers start: 78 outliers final: 43 residues processed: 166 average time/residue: 0.1544 time to fit residues: 42.0777 Evaluate side-chains 129 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 72 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 193 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 238 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B1036 GLN C 115 GLN C 370 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.080372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.053177 restraints weight = 120510.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.054896 restraints weight = 59081.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.055918 restraints weight = 38795.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.056601 restraints weight = 29809.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.057007 restraints weight = 25409.005| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26802 Z= 0.197 Angle : 0.786 19.683 36614 Z= 0.373 Chirality : 0.049 0.593 4308 Planarity : 0.006 0.129 4689 Dihedral : 8.329 63.842 4392 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.75 % Favored : 87.07 % Rotamer: Outliers : 2.67 % Allowed : 17.35 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.14), residues: 3317 helix: 1.35 (0.21), residues: 685 sheet: -1.96 (0.21), residues: 607 loop : -2.87 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 61 TYR 0.031 0.002 TYR A 369 PHE 0.023 0.002 PHE C 855 TRP 0.015 0.002 TRP B 104 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00445 (26733) covalent geometry : angle 0.74100 (36449) SS BOND : bond 0.00812 ( 42) SS BOND : angle 1.60227 ( 84) hydrogen bonds : bond 0.04121 ( 707) hydrogen bonds : angle 5.40759 ( 1977) link_BETA1-4 : bond 0.00617 ( 2) link_BETA1-4 : angle 2.74638 ( 6) link_NAG-ASN : bond 0.00812 ( 25) link_NAG-ASN : angle 5.60724 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 73 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.6799 (m110) REVERT: A 429 PHE cc_start: 0.8578 (t80) cc_final: 0.7853 (t80) REVERT: A 450 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8336 (p0) REVERT: A 697 MET cc_start: 0.8803 (ttp) cc_final: 0.8542 (ttp) REVERT: A 740 MET cc_start: 0.8461 (tmm) cc_final: 0.7902 (tmm) REVERT: A 802 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8784 (p90) REVERT: A 851 CYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8360 (t) REVERT: B 69 HIS cc_start: 0.7129 (OUTLIER) cc_final: 0.6373 (m-70) REVERT: B 104 TRP cc_start: 0.6925 (OUTLIER) cc_final: 0.5870 (p-90) REVERT: B 215 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5404 (m-30) REVERT: B 740 MET cc_start: 0.9192 (tpt) cc_final: 0.8903 (tpp) REVERT: B 1132 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8840 (pt) REVERT: C 201 PHE cc_start: 0.8240 (t80) cc_final: 0.7887 (t80) REVERT: C 387 LEU cc_start: 0.9106 (mm) cc_final: 0.8900 (mp) REVERT: C 488 CYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5797 (t) REVERT: C 697 MET cc_start: 0.8722 (ttp) cc_final: 0.8311 (ttm) REVERT: C 921 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8354 (tptt) REVERT: C 1107 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7689 (tpm170) REVERT: L 78 LEU cc_start: -0.0340 (tp) cc_final: -0.0881 (mm) outliers start: 75 outliers final: 46 residues processed: 143 average time/residue: 0.1743 time to fit residues: 41.3509 Evaluate side-chains 122 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 65 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 2 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 152 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 chunk 224 optimal weight: 0.0000 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 173 optimal weight: 0.0670 chunk 162 optimal weight: 3.9990 overall best weight: 2.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.079766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052746 restraints weight = 120167.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.054364 restraints weight = 58447.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.055451 restraints weight = 38090.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.056117 restraints weight = 29270.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.056515 restraints weight = 24939.480| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 26802 Z= 0.196 Angle : 0.769 19.571 36614 Z= 0.365 Chirality : 0.049 0.561 4308 Planarity : 0.005 0.093 4689 Dihedral : 8.132 59.815 4388 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.06 % Favored : 87.79 % Rotamer: Outliers : 2.92 % Allowed : 17.18 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.14), residues: 3317 helix: 1.34 (0.21), residues: 692 sheet: -1.97 (0.21), residues: 589 loop : -2.81 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1019 TYR 0.030 0.001 TYR A 369 PHE 0.033 0.002 PHE A 559 TRP 0.016 0.002 TRP B 64 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00446 (26733) covalent geometry : angle 0.72516 (36449) SS BOND : bond 0.00451 ( 42) SS BOND : angle 1.40802 ( 84) hydrogen bonds : bond 0.03971 ( 707) hydrogen bonds : angle 5.38526 ( 1977) link_BETA1-4 : bond 0.00841 ( 2) link_BETA1-4 : angle 3.28204 ( 6) link_NAG-ASN : bond 0.00802 ( 25) link_NAG-ASN : angle 5.50157 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 67 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.6864 (m110) REVERT: A 378 LYS cc_start: 0.8180 (tptp) cc_final: 0.7874 (tptp) REVERT: A 402 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7738 (pt) REVERT: A 421 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7835 (m-10) REVERT: A 429 PHE cc_start: 0.8491 (t80) cc_final: 0.7629 (t80) REVERT: A 450 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8286 (p0) REVERT: A 562 PHE cc_start: 0.7270 (p90) cc_final: 0.6818 (p90) REVERT: A 740 MET cc_start: 0.8432 (tmm) cc_final: 0.7865 (tmm) REVERT: A 851 CYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 69 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6436 (m-70) REVERT: B 104 TRP cc_start: 0.6802 (OUTLIER) cc_final: 0.5880 (p-90) REVERT: B 115 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6984 (mm-40) REVERT: B 215 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.6135 (m-30) REVERT: B 1029 MET cc_start: 0.9478 (tpp) cc_final: 0.8995 (tpp) REVERT: B 1071 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8105 (tp40) REVERT: B 1132 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8889 (pt) REVERT: C 88 ASP cc_start: 0.8608 (t0) cc_final: 0.8400 (t0) REVERT: C 201 PHE cc_start: 0.8374 (t80) cc_final: 0.8115 (t80) REVERT: C 389 ASP cc_start: 0.9174 (m-30) cc_final: 0.8785 (p0) REVERT: C 488 CYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5609 (t) REVERT: C 697 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8261 (ttm) REVERT: C 921 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8416 (tptt) REVERT: H 110 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7875 (pm20) REVERT: L 20 THR cc_start: 0.5572 (t) cc_final: 0.5334 (m) REVERT: L 78 LEU cc_start: 0.0126 (tp) cc_final: -0.0528 (mm) outliers start: 82 outliers final: 56 residues processed: 143 average time/residue: 0.1573 time to fit residues: 36.6577 Evaluate side-chains 134 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 64 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 163 optimal weight: 0.2980 chunk 107 optimal weight: 0.3980 chunk 213 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 294 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 286 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.080446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.053649 restraints weight = 119491.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055358 restraints weight = 57050.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056467 restraints weight = 36754.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057154 restraints weight = 27995.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.057574 restraints weight = 23745.079| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26802 Z= 0.128 Angle : 0.725 19.110 36614 Z= 0.342 Chirality : 0.048 0.539 4308 Planarity : 0.005 0.085 4689 Dihedral : 7.876 59.752 4388 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.61 % Favored : 88.24 % Rotamer: Outliers : 2.28 % Allowed : 17.85 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.15), residues: 3317 helix: 1.54 (0.21), residues: 693 sheet: -1.90 (0.21), residues: 590 loop : -2.69 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1019 TYR 0.029 0.001 TYR A 369 PHE 0.020 0.001 PHE B 490 TRP 0.015 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00289 (26733) covalent geometry : angle 0.68173 (36449) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.13083 ( 84) hydrogen bonds : bond 0.03721 ( 707) hydrogen bonds : angle 5.17483 ( 1977) link_BETA1-4 : bond 0.00570 ( 2) link_BETA1-4 : angle 3.25672 ( 6) link_NAG-ASN : bond 0.00817 ( 25) link_NAG-ASN : angle 5.33089 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 75 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.6799 (m110) REVERT: A 106 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8145 (p90) REVERT: A 187 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7254 (mmtt) REVERT: A 389 ASP cc_start: 0.8630 (m-30) cc_final: 0.8305 (m-30) REVERT: A 402 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7701 (pt) REVERT: A 429 PHE cc_start: 0.8566 (t80) cc_final: 0.7789 (t80) REVERT: A 740 MET cc_start: 0.8388 (tmm) cc_final: 0.7827 (tmm) REVERT: A 851 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8222 (t) REVERT: B 69 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6278 (m-70) REVERT: B 104 TRP cc_start: 0.6810 (OUTLIER) cc_final: 0.5955 (p-90) REVERT: B 115 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6985 (mm-40) REVERT: B 215 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6188 (m-30) REVERT: B 380 TYR cc_start: 0.8011 (m-80) cc_final: 0.7582 (m-80) REVERT: B 574 ASP cc_start: 0.8457 (m-30) cc_final: 0.8177 (m-30) REVERT: B 1029 MET cc_start: 0.9452 (tpp) cc_final: 0.8993 (tpp) REVERT: C 201 PHE cc_start: 0.8305 (t80) cc_final: 0.8041 (t80) REVERT: C 387 LEU cc_start: 0.9047 (mm) cc_final: 0.8822 (mt) REVERT: C 488 CYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5702 (t) REVERT: C 697 MET cc_start: 0.8651 (ttp) cc_final: 0.8283 (ttm) REVERT: C 921 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8310 (tptp) REVERT: C 1107 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7690 (tpm170) REVERT: C 1134 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8396 (p0) REVERT: L 18 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.3068 (tpt90) REVERT: L 20 THR cc_start: 0.5880 (t) cc_final: 0.5497 (t) REVERT: L 78 LEU cc_start: 0.0095 (tp) cc_final: -0.0387 (mm) outliers start: 64 outliers final: 42 residues processed: 138 average time/residue: 0.1887 time to fit residues: 42.3477 Evaluate side-chains 124 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 68 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 76 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 246 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 132 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.080234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053458 restraints weight = 119789.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055152 restraints weight = 57278.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.056268 restraints weight = 36865.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.056943 restraints weight = 28090.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.057352 restraints weight = 23848.301| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26802 Z= 0.138 Angle : 0.723 18.956 36614 Z= 0.340 Chirality : 0.047 0.522 4308 Planarity : 0.005 0.081 4689 Dihedral : 7.759 59.841 4384 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.37 % Favored : 88.48 % Rotamer: Outliers : 2.31 % Allowed : 18.17 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.15), residues: 3317 helix: 1.55 (0.21), residues: 693 sheet: -1.83 (0.21), residues: 596 loop : -2.66 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1019 TYR 0.031 0.001 TYR A 369 PHE 0.021 0.001 PHE B 490 TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (26733) covalent geometry : angle 0.68112 (36449) SS BOND : bond 0.00326 ( 42) SS BOND : angle 1.12923 ( 84) hydrogen bonds : bond 0.03679 ( 707) hydrogen bonds : angle 5.15014 ( 1977) link_BETA1-4 : bond 0.00507 ( 2) link_BETA1-4 : angle 3.12600 ( 6) link_NAG-ASN : bond 0.00801 ( 25) link_NAG-ASN : angle 5.24478 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 69 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.6806 (m110) REVERT: A 106 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8147 (p90) REVERT: A 187 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7225 (mmtt) REVERT: A 389 ASP cc_start: 0.8597 (m-30) cc_final: 0.8253 (m-30) REVERT: A 402 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7659 (pt) REVERT: A 429 PHE cc_start: 0.8543 (t80) cc_final: 0.7699 (t80) REVERT: A 740 MET cc_start: 0.8401 (tmm) cc_final: 0.7842 (tmm) REVERT: B 69 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.6239 (m-70) REVERT: B 104 TRP cc_start: 0.6699 (OUTLIER) cc_final: 0.5785 (p-90) REVERT: B 115 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7031 (mm-40) REVERT: B 215 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6374 (m-30) REVERT: B 574 ASP cc_start: 0.8454 (m-30) cc_final: 0.8171 (m-30) REVERT: B 1029 MET cc_start: 0.9459 (tpp) cc_final: 0.9009 (tpp) REVERT: B 1132 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8895 (pt) REVERT: C 201 PHE cc_start: 0.8311 (t80) cc_final: 0.8029 (t80) REVERT: C 389 ASP cc_start: 0.9182 (m-30) cc_final: 0.8780 (p0) REVERT: C 488 CYS cc_start: 0.5268 (OUTLIER) cc_final: 0.5012 (t) REVERT: C 697 MET cc_start: 0.8641 (ttp) cc_final: 0.8251 (ttm) REVERT: C 786 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8754 (pttm) REVERT: C 869 MET cc_start: 0.8678 (ptp) cc_final: 0.8185 (pmm) REVERT: C 921 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8309 (tptp) REVERT: C 1107 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7708 (tpm170) REVERT: C 1134 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8418 (p0) REVERT: L 18 ARG cc_start: 0.4886 (OUTLIER) cc_final: 0.2985 (tpt90) REVERT: L 20 THR cc_start: 0.5709 (t) cc_final: 0.5476 (t) REVERT: L 78 LEU cc_start: 0.0337 (tp) cc_final: -0.0196 (mm) outliers start: 65 outliers final: 44 residues processed: 131 average time/residue: 0.1855 time to fit residues: 39.7483 Evaluate side-chains 124 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 66 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1134 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 299 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 333 optimal weight: 40.0000 chunk 153 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.080305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.053566 restraints weight = 119511.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.055299 restraints weight = 57219.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.056424 restraints weight = 36783.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057067 restraints weight = 28045.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057487 restraints weight = 23931.114| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26802 Z= 0.133 Angle : 0.713 18.569 36614 Z= 0.336 Chirality : 0.047 0.494 4308 Planarity : 0.005 0.074 4689 Dihedral : 7.600 59.306 4384 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.40 % Favored : 88.45 % Rotamer: Outliers : 2.03 % Allowed : 18.39 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.15), residues: 3317 helix: 1.59 (0.21), residues: 694 sheet: -1.73 (0.21), residues: 586 loop : -2.57 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1019 TYR 0.030 0.001 TYR A 369 PHE 0.022 0.001 PHE B 490 TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00301 (26733) covalent geometry : angle 0.67338 (36449) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.06601 ( 84) hydrogen bonds : bond 0.03623 ( 707) hydrogen bonds : angle 5.09679 ( 1977) link_BETA1-4 : bond 0.00473 ( 2) link_BETA1-4 : angle 3.10414 ( 6) link_NAG-ASN : bond 0.00790 ( 25) link_NAG-ASN : angle 5.08580 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6359.89 seconds wall clock time: 110 minutes 3.67 seconds (6603.67 seconds total)